Cryptococcus albidus keratitis is a rare and difficult diagnosed disease. Here we report a case of C albidus keratitis early diagnosed by dot hybridization assay and successfully treated with intrastromal injection of Amphotericin B (AB).A 45-year-old man presented with left red eye for 2 days. The slit lamp examination exhibited deep corneal infiltrations. Smears and cultures were performed but revealed negative findings. Molecular detection of pathogens was performed by dot hybridization assay, and C albidus keratitis was diagnosed. Despite the identification of C albidus, the clinical condition still worsened due to deep corneal infiltration. After performing intrastromal injection of AB, the corneal infiltration gradually improved.C albidus is a rare cause of diseases in humans and should be considered as a potential pathogen of corneal ulcer. The prognosis of C albidus keratitis will improve if the condition is recognized early and treated properly.